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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs11240779

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:873251 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.452170 (119685/264690, TOPMED)
G=0.438062 (61369/140092, GnomAD)
G=0.34923 (6597/18890, ALFA) (+ 13 more)
A=0.34427 (5770/16760, 8.3KJPN)
A=0.4535 (2271/5008, 1000G)
G=0.2231 (860/3854, ALSPAC)
G=0.2303 (854/3708, TWINSUK)
A=0.3727 (1092/2930, KOREAN)
A=0.3592 (658/1832, Korea1K)
G=0.252 (251/998, GoNL)
G=0.202 (121/600, NorthernSweden)
G=0.249 (133/534, MGP)
G=0.296 (110/372, SGDP_PRJ)
A=0.495 (107/216, Qatari)
A=0.486 (103/212, Vietnamese)
G=0.29 (14/48, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FAM41C : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 1 NC_000001.11:g.873251G>A
GRCh37.p13 chr 1 NC_000001.10:g.808631G>A
TUBB8P11 pseudogene NG_005336.4:g.61G>A
Gene: FAM41C, family with sequence similarity 41 member C (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FAM41C transcript NR_027055.1:n. N/A Intron Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.34923 A=0.65077
European Sub 14286 G=0.24864 A=0.75136
African Sub 2946 G=0.8007 A=0.1993
African Others Sub 114 G=0.921 A=0.079
African American Sub 2832 G=0.7959 A=0.2041
Asian Sub 112 G=0.545 A=0.455
East Asian Sub 86 G=0.57 A=0.43
Other Asian Sub 26 G=0.46 A=0.54
Latin American 1 Sub 146 G=0.493 A=0.507
Latin American 2 Sub 610 G=0.344 A=0.656
South Asian Sub 98 G=0.47 A=0.53
Other Sub 692 G=0.429 A=0.571


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.452170 A=0.547830
gnomAD - Genomes Global Study-wide 140092 G=0.438062 A=0.561938
gnomAD - Genomes European Sub 75872 G=0.25397 A=0.74603
gnomAD - Genomes African Sub 41974 G=0.80109 A=0.19891
gnomAD - Genomes American Sub 13654 G=0.37132 A=0.62868
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.2225 A=0.7775
gnomAD - Genomes East Asian Sub 3124 G=0.5647 A=0.4353
gnomAD - Genomes Other Sub 2146 G=0.4203 A=0.5797
8.3KJPN JAPANESE Study-wide 16760 G=0.65573 A=0.34427
1000Genomes Global Study-wide 5008 G=0.5465 A=0.4535
1000Genomes African Sub 1322 G=0.8850 A=0.1150
1000Genomes East Asian Sub 1008 G=0.5833 A=0.4167
1000Genomes Europe Sub 1006 G=0.2276 A=0.7724
1000Genomes South Asian Sub 978 G=0.520 A=0.480
1000Genomes American Sub 694 G=0.347 A=0.653
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2231 A=0.7769
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2303 A=0.7697
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6273 A=0.3727
Korean Genome Project KOREAN Study-wide 1832 G=0.6408 A=0.3592
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.252 A=0.748
Northern Sweden ACPOP Study-wide 600 G=0.202 A=0.798
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.249 A=0.751
SGDP_PRJ Global Study-wide 372 G=0.296 A=0.704
Qatari Global Study-wide 216 G=0.505 A=0.495
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.514 A=0.486
Siberian Global Study-wide 48 G=0.29 A=0.71
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement G= A
GRCh38.p13 chr 1 NC_000001.11:g.873251= NC_000001.11:g.873251G>A
GRCh37.p13 chr 1 NC_000001.10:g.808631= NC_000001.10:g.808631G>A
TUBB8P11 pseudogene NG_005336.4:g.61= NG_005336.4:g.61G>A
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

61 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16439576 Feb 27, 2004 (120)
2 SC_SNP ss18282238 Feb 27, 2004 (120)
3 SSAHASNP ss20579670 Apr 05, 2004 (121)
4 ABI ss41345311 Mar 15, 2006 (126)
5 HGSV ss82925691 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss87156187 Mar 23, 2008 (129)
7 HUMANGENOME_JCVI ss97913281 Feb 04, 2009 (130)
8 BGI ss105111743 Feb 04, 2009 (130)
9 1000GENOMES ss107938298 Jan 22, 2009 (130)
10 ENSEMBL ss131815891 Dec 01, 2009 (131)
11 GMI ss154522499 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss162980938 Jul 04, 2010 (132)
13 BUSHMAN ss197885549 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss205423221 Jul 04, 2010 (132)
15 1000GENOMES ss218190501 Jul 14, 2010 (132)
16 1000GENOMES ss230395513 Jul 14, 2010 (132)
17 1000GENOMES ss238115033 Jul 15, 2010 (132)
18 BL ss252864211 May 09, 2011 (134)
19 GMI ss275681001 May 04, 2012 (137)
20 GMI ss283987435 Apr 25, 2013 (138)
21 PJP ss290493849 May 09, 2011 (134)
22 TISHKOFF ss553710705 Apr 25, 2013 (138)
23 SSMP ss647516519 Apr 25, 2013 (138)
24 EVA-GONL ss974769673 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1067612463 Aug 21, 2014 (142)
26 1000GENOMES ss1289340553 Aug 21, 2014 (142)
27 DDI ss1425684986 Apr 01, 2015 (144)
28 EVA_DECODE ss1584129680 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1599378623 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1642372656 Apr 01, 2015 (144)
31 EVA_MGP ss1710883397 Apr 01, 2015 (144)
32 WEILL_CORNELL_DGM ss1917960891 Feb 12, 2016 (147)
33 GENOMED ss1966667369 Jul 19, 2016 (147)
34 JJLAB ss2019498522 Sep 14, 2016 (149)
35 USC_VALOUEV ss2147484496 Dec 20, 2016 (150)
36 TOPMED ss2321505709 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2624264839 Nov 08, 2017 (151)
38 GRF ss2697374952 Nov 08, 2017 (151)
39 GNOMAD ss2750642517 Nov 08, 2017 (151)
40 SWEGEN ss2986149618 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3023513724 Nov 08, 2017 (151)
42 TOPMED ss3066407979 Nov 08, 2017 (151)
43 CSHL ss3343272760 Nov 08, 2017 (151)
44 OMUKHERJEE_ADBS ss3646218716 Oct 11, 2018 (152)
45 URBANLAB ss3646581278 Oct 11, 2018 (152)
46 EVA_DECODE ss3685992600 Jul 12, 2019 (153)
47 ACPOP ss3726716581 Jul 12, 2019 (153)
48 EVA ss3745721273 Jul 12, 2019 (153)
49 PACBIO ss3783302213 Jul 12, 2019 (153)
50 PACBIO ss3788980086 Jul 12, 2019 (153)
51 PACBIO ss3793852620 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3798743963 Jul 12, 2019 (153)
53 EVA ss3825981536 Apr 25, 2020 (154)
54 EVA ss3836378484 Apr 25, 2020 (154)
55 EVA ss3841782489 Apr 25, 2020 (154)
56 SGDP_PRJ ss3847996375 Apr 25, 2020 (154)
57 KRGDB ss3892836680 Apr 25, 2020 (154)
58 KOGIC ss3943630262 Apr 25, 2020 (154)
59 TOPMED ss4436442341 Apr 25, 2021 (155)
60 TOMMO_GENOMICS ss5142053782 Apr 25, 2021 (155)
61 EVA ss5237158324 Apr 25, 2021 (155)
62 1000Genomes NC_000001.10 - 808631 Oct 11, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 808631 Oct 11, 2018 (152)
64 gnomAD - Genomes NC_000001.11 - 873251 Apr 25, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000001.10 - 808631 Apr 25, 2020 (154)
66 KOREAN population from KRGDB NC_000001.10 - 808631 Apr 25, 2020 (154)
67 Korean Genome Project NC_000001.11 - 873251 Apr 25, 2020 (154)
68 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 808631 Apr 25, 2020 (154)
69 Northern Sweden NC_000001.10 - 808631 Jul 12, 2019 (153)
70 Qatari NC_000001.10 - 808631 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000001.10 - 808631 Apr 25, 2020 (154)
72 Siberian NC_000001.10 - 808631 Apr 25, 2020 (154)
73 8.3KJPN NC_000001.10 - 808631 Apr 25, 2021 (155)
74 TopMed NC_000001.11 - 873251 Apr 25, 2021 (155)
75 UK 10K study - Twins NC_000001.10 - 808631 Oct 11, 2018 (152)
76 A Vietnamese Genetic Variation Database NC_000001.10 - 808631 Jul 12, 2019 (153)
77 ALFA NC_000001.11 - 873251 Apr 25, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs57633625 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82925691 NC_000001.8:848493:G:A NC_000001.11:873250:G:A (self)
ss87156187, ss107938298, ss162980938, ss197885549, ss205423221, ss252864211, ss275681001, ss283987435, ss290493849, ss1584129680 NC_000001.9:798493:G:A NC_000001.11:873250:G:A (self)
5332, 603, 698, 14074, 149, 1446, 2821, 13355, 850, 23089, 603, 123, ss218190501, ss230395513, ss238115033, ss553710705, ss647516519, ss974769673, ss1067612463, ss1289340553, ss1425684986, ss1599378623, ss1642372656, ss1710883397, ss1917960891, ss1966667369, ss2019498522, ss2147484496, ss2321505709, ss2624264839, ss2697374952, ss2750642517, ss2986149618, ss3343272760, ss3646218716, ss3726716581, ss3745721273, ss3783302213, ss3788980086, ss3793852620, ss3825981536, ss3836378484, ss3847996375, ss3892836680, ss5142053782 NC_000001.10:808630:G:A NC_000001.11:873250:G:A (self)
73296, 8263, 22816, 48676, 13893891782, ss3023513724, ss3066407979, ss3646581278, ss3685992600, ss3798743963, ss3841782489, ss3943630262, ss4436442341, ss5237158324 NC_000001.11:873250:G:A NC_000001.11:873250:G:A (self)
ss41345311, ss97913281, ss105111743, ss131815891, ss154522499 NT_004350.19:287262:G:A NC_000001.11:873250:G:A (self)
ss16439576, ss18282238, ss20579670 NT_034471.3:287262:G:A NC_000001.11:873250:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs11240779

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad